Did you read that little detail about game A and B? You'll never get a shiny Manaphy on the game the egg is received. The change in nature is the shiny check at work. There are also two hexflawless Modest spreads so it's possible you aren't actually using the one that's paired with Timid, which is why the nature turns out fine.
Last edited by Everstone; Oct 8th, 2012 at 11:07:22 AM.